The Military

It is confirmed that the military(if you can still even call it that) is also tracking Joel and Ellie's progress through the post-apocalyptic United States. Under a new "martial law," the military aims to contain all uninfected life to various quarantine zones across the country. Life in these zones is a brutal existence, living in constant fear of the fungus and the outside world. There are regular checkpoints throughout these zones where the population is inspected for signs of the infection. If tested positive, the individual is immediately euthanized. All of this is run by the military.

Although exact details are not known at this time, it is certain that the military will play a large factor in the day-to-day life of Joel and Ellie. It is suspected that Joel has a previous history and some bad-blood with the military.